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Abstract

A Gram-stain-negative bacterium, designated strain 40Bstr34, isolated from a sediment sample from the West Pacific Ocean, was taxonomically characterized by using a polyphasic approach. The strain was phylogenetically close to LZB041 and CBS5Q-3, with 16S rRNA gene sequence similarities of 98.5 and 97.1 %, respectively. The genome of strain 40Bstr34 featured a G+C content of 65.7 % for a 5.8 Mb chromosome. Up-to-date bacterial core gene set analysis revealed that strain 40Bstr34 represents one independent lineage with LZB041. DNA–DNA hybridization values between strain 40Bstr34 and its phylogenetic neighbours ranged from 30.3–34.2 %, below the cutoff of 70 %. In addition, the corresponding average nucleotide identity values were between 81.8–83.7 %, which are lower than 95 % threshold. The predominant cellular fatty acids of strain 40Bstr34 were summed feature 8 (C ω and/or C ω), cyclo-C ω8 and iso-C 3-OH, and ubiquinone-10 as the predominant respiratory quinone. The major polar lipids included phosphatidylethanolamine, phosphatidylmonomethylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, two unidentified aminolipids and two unidentified lipids. Based on the results of phenotypic, chemotaxonomic and genetic analyses, strain 40Bstr34 is identified as representing a novel species of the genus for which the name sp. nov. is proposed. The type strain is 40Bstr34 (=JCM 33903=MCCC 1K04569).

Funding
This study was supported by the:
  • Key Science and Technology Program of Ningbo City (Award 2012C10038)
    • Principle Award Recipient: Jifang Yang
  • Scientific Research Fund of the Second Institute of Oceanography, MNR (Award JG1418)
    • Principle Award Recipient: Jigang Chen
  • Zhejiang Provincial Top Key Discipline of Biological Engineering (Award CX2018019)
    • Principle Award Recipient: Zehao Xue
  • China Ocean Mineral Resources Research and Development Association (Award DY135-E2-02-07)
    • Principle Award Recipient: Jigang Chen
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2020-06-25
2024-03-29
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References

  1. Liang J, Liu J, Zhang X-H. Jiella aquimaris gen. nov., sp. nov., isolated from offshore surface seawater. Int J Syst Evol Microbiol 2015; 65:1127–1132 [View Article][PubMed]
    [Google Scholar]
  2. Tuo L, Yan X-R, Xiao J-H. Jiella endophytica sp. nov., a novel endophytic bacterium isolated from root of Ficus microcarpa Linn. f . Antonie Van Leeuwenhoek 2019; 112:1457–1463 [View Article][PubMed]
    [Google Scholar]
  3. Li A-Z, Lin L-Z, Zhang M-X, Zhu H-H. Aurantimonas aggregata sp. nov., isolated from deep-sea sediment. Int J Syst Evol Microbiol 2017; 67:5056–5061 [View Article][PubMed]
    [Google Scholar]
  4. Bernardet JF, Nakagawa Y, Holmes B. Subcommittee on the taxonomy of Flavobacterium and Cytophaga-like bacteria of the International Committee on Systematics of Prokaryotes. Proposed minimal standards for describing new taxa of the family Flavobacteriaceae and emended description of the family. Int J Syst Evol Microbiol 2002; 52:1049–1070
    [Google Scholar]
  5. Gosink JJ, Woese CR, Staley JT. Polaribacter gen. nov., with three new species, P. irgensii sp. nov., P. franzmannii sp. nov. and P. filamentus sp. nov., gas vacuolate polar marine bacteria of the Cytophaga-Flavobacterium-Bacteroides group and reclassification of 'Flectobacillus glomeratus' as Polaribacter glomeratus comb. nov. Int J Syst Bacteriol 1998; 8:223–235 [View Article][PubMed]
    [Google Scholar]
  6. Chen Y, Zhu S, Lin D, Wang X, Yang J et al. Devosia naphthalenivorans sp. nov., isolated from East Pacific Ocean sediment. Int J Syst Evol Microbiol 2019; 69:1974–1979 [View Article][PubMed]
    [Google Scholar]
  7. Wang X, Lin D, Jing X, Zhu S, Yang J et al. Complete genome sequence of the highly Mn(II) tolerant Staphylococcus sp. AntiMn-1 isolated from deep-sea sediment in the Clarion-Clipperton Zone. J Biotechnol 2018; 266:34–38 [View Article][PubMed]
    [Google Scholar]
  8. Lane DJ. 16S/23S rRNA sequencing. In Stackebrandt E, Goodfellow M. (editors) Nucleic Acid Techniques in Bacterial Systematics Chichester, United Kingdom: John Wiley & Sons; 1991 pp 115–175
    [Google Scholar]
  9. Yoon S-H, Ha S-M, Kwon S, Lim J, Kim Y et al. Introducing EzBioCloud: a taxonomically United database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 2017; 67:1613–1617 [View Article][PubMed]
    [Google Scholar]
  10. Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016; 33:1870–1874 [View Article][PubMed]
    [Google Scholar]
  11. Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 1980; 16:111–120 [View Article][PubMed]
    [Google Scholar]
  12. Nei M, Kumar S. Molecular Evolution and Phylogenetics New York: Oxford University Press; 2000
    [Google Scholar]
  13. Na S-I, Kim YO, Yoon S-H, Ha S-M, Baek I et al. UBCG: up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction. J Microbiol 2018; 56:280–285 [View Article][PubMed]
    [Google Scholar]
  14. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014; 30:2068–2069 [View Article][PubMed]
    [Google Scholar]
  15. Nordberg H, Cantor M, Dusheyko S, Hua S, Poliakov A et al. The genome portal of the Department of energy joint genome Institute: 2014 updates. Nucleic Acids Res 2014; 42:D26–D31 [View Article][PubMed]
    [Google Scholar]
  16. Yoon S-H, Ha S-M, Lim J, Kwon S, Chun J. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie van Leeuwenhoek 2017; 110:1281–1286 [View Article][PubMed]
    [Google Scholar]
  17. Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [View Article][PubMed]
    [Google Scholar]
  18. Colston SM, Fullmer MS, Beka L, Lamy B, Gogarten JP et al. Bioinformatic genome comparisons for taxonomic and phylogenetic assignments using Aeromonas as a test case. mBio 2014; 5:e02136–14 [View Article][PubMed]
    [Google Scholar]
  19. Chun J, Oren A, Ventosa A, Christensen H, Arahal DR et al. Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 2018; 68:461–466 [View Article][PubMed]
    [Google Scholar]
  20. Komagata K, Suzuki K. Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 1987; 19:161–207
    [Google Scholar]
  21. da Costa MS, Albuquerque L, Nobre MF, Wait R. The identification of polar lipids in prokaryotes. Methods Microbiol 2011; 38:165–181
    [Google Scholar]
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